<div dir="ltr"><p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman","serif"">Hello,</span></p>
<p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:12pt"><span style="font-size:12pt;font-family:"Times New Roman","serif"">My name is Ian and I am new to the
bioinformatics world. I am using the biopython's melting temp TM_NN algorithm
to calculate the melting temp differences in wild type sequence with the
complementary mutation sequence, using the the the Allawi and SantaLucia
(1997), Biochemistry 36: 10581-10594 table. I have attached a small output of
the sample program for better understanding, which shows the Key Error I am
getting and other times I will get a Value Error, meaning it can find the key
but can't find the value, I was wondering if </span></p>
<p class="MsoNormal" style="margin-bottom:12pt"><span style="font-size:12pt;font-family:"Times New Roman","serif"">A) if there is something else out there
better suited for this problem</span></p>
<p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman","serif"">B)
if I need to update the table or something to get working and if so how would I
go about improving the dictionary being used to address the problems which can be seen here</span></p><p class="MsoNormal"><br><span style="font-size:12pt;font-family:"Times New Roman","serif"">/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931:
BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be
wrong<br> BiopythonWarning)</span></p><p class="MsoNormal"><br><span style="font-size:12pt;font-family:"Times New Roman","serif""></span></p><p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman","serif"">Here is the output of the code. I think that the '.' may be equivalent to the regex expression of '.' meaning it could be any character in front of the G. But as you can see it is not a problem for the one up above. </span> </p><p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman","serif""><br></span></p><p class="MsoNormal"><span style="font-size:12pt;font-family:"Times New Roman","serif"">seq: ['G', 'A', 'T']<br>Mutation c_seq: ['C', 'C', 'A']<br>/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py:931: BiopythonWarning: no data for neighbors 'AT/AG'. Calculation will be wrong<br> BiopythonWarning)<br>TM: -262.480685148<br>seq: ['G', 'A', 'T', 'A']<br>Mutation c_seq: ['C', 'C', 'A', 'T']<br>Traceback (most recent call last):<br> File "PrimerBuilder.py", line 333, in <module><br> switchList = switchBuilder(middle,basepairs,mutation)<br> File "PrimerBuilder.py", line 56, in switchBuilder<br> tmMismatch = mt.Tm_NN(switch,strict=False,c_seq=mutation,nn_table=mt.DNA_NN3)<br> File "/Library/Python/2.7/site-packages/Bio/SeqUtils/MeltingTemp.py", line 856, in Tm_NN<br> deltaH += de_table[right_de][dH]<br>KeyError: '.G/AT'<br><br></span></p></div>